PRIMER PICKING RESULTS FOR NM_006162_10p5 Using mispriming library /data/utswmc/elxr/ELXR-main/repbase/humrep_and_simple.fa Using 0-based sequence positions OLIGO start len tm gc% any 3' rep seq LEFT PRIMER 1847 20 59.90 50.00 6.00 2.00 11.00 CACAATCGCGTCTCTTGTGT RIGHT PRIMER 2339 21 60.33 52.38 7.00 1.00 12.00 ttacagggcctgggaactatc SEQUENCE SIZE: 2395 INCLUDED REGION SIZE: 2395 PRODUCT SIZE: 493, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 0.00 TARGETS (start, len)*: 1869,400 EXCLUDED REGIONS (start, len)*: 0,1569 2395,0 0 cagcatcttcccagcatcgcggccggcacctggcacctgcactttggccgtcagagacgt XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 60 gctggtaccgtgctacggacgagggcggtcactctggcgaccccagctctctgccgaggc XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 agccaggcactggctcacgacactcatggaccagggtgggaccgaggaggaaatgtgggt XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 180 tcctggggagatgccttgtcacaggcgtgagcgtcactgatggagaagcagggctggggg XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 240 cgttgctttgatgtttatggtatttctctaatactttctcaatttttcttttcttacagT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 300 AAATGAAATAATACGAAATGACCTCTCCAGCACGAGCACCCACTCCTAGTTGCCACATTG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 360 GAGCACTCAGTTCAGCAGGGGTATGCTGACTTCAGCAGACAAAGACTTTTGAATAAATAA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 420 ACTGAACTCACACCTGGTACCACTCAGAACCTCCAACTGACTGAATGCCAGGAGCTGAAC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 480 ATTAATATGTGCAAAGATTGGCTCTCCAACAAGAAGGAAAGCAGGGAGGAAGGGAGACCA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 540 CTGTGTCACCTGGAGGAGAAGTCATCTCATGACAACAGAAGGGAGGTGGCCGGGCTGAGC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 600 ACGGGAGACCCACCGTGCAGGGGCCTTTCATGGGAACGGCCCACACGCAGTTTGACCCCA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 660 CGCCCAGCCCTTCTGGCACCCCTGGGGTTCAATACTGGAAGTGCCTTATTTAACCAGACC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 720 ATCAGGGCATCATAGAATTGAGCATTGAATTTGCTACTGTAGGAGTATTTTTAGGAGCAG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 780 AAACTGCAAACACATTTCATTGTGAGGTTTTACCCTCTGTATGAATGAAGAGAACGCTGG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 840 AAGGCTGCGAGAGGACTCTAGTATGAGTCTCCAACATTTGGAACGTTTCCTGGGCTGTCA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 900 CGTACACTCCTGCTGCCTTACACAGTGCATTTTAGAATCTTCCAGTCTGTCATCTCAGCT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 960 CTTTTGTAACATGCTTCCCTTGTCTGCGCGGTTGAAACCGTAGGCTTGTTCATAGTCGCA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1020 TGCTCGCATCTTTGTTTTTAATCTGGCTTCGAACATAGCACAAGTAACTTGAATAGCACA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1080 TCAATAGGTTACTGGACAAAAGCAGAAAAACCTGTTACAGGATAGCCTGCATTTGCATGT XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1140 GTGTACATATCTAGGCATCTATTTATGTATAAATAATAACAGAGCCGACGTGTCCTCGCC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1200 CAGGAGGGCTTCCCTGTCAGCAATAACCGGCATCCGTTTTGGAACCTGCGTCTGGGGCTC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1260 CAGTCGCTGCTCTTGCTGGCGTCCATCGCCGCCTCGGACGGCCGTGCATTTTCTCGTCTC XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1320 ACGCAGTTCGAGGAGGACCCTAGAAAGCCAGGAGCTGTGATTGACAGTAGCTGTAGGTTA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1380 CCAGACGGCAACATTAGAAAGTGATTGTAAATAACATGCAACCTAAGTGTAATATATTTG XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1440 TTCAGTTATAAGATGATTGTTTCACAGAAGCCTTACCACTCTCTGCTTCATCTAAGAAAA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1500 CCAATACCAAAAACGCCACTTTAATGCTCAGCCCTGCGTTGTGTGTTTTCAGATGAGTTA XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1560 CTGTTAACAGGTAGGTTTGTGTAGGCCTTGCTGGGCACTCTGTACAATTAGTTGCTTATT XXXXXXXXX 1620 ACGTATGATTACTCACAGCGATCTATTGTTCCATATAACCAAAAAGCATGGTTTATTCAT 1680 TGAAACACGGTTGACCTGAACTCGTGCCTTAGGAATTAATGCCCCCTTATGGAACCTGCC 1740 TGAATTGCACCTGCGGGTGGAGGCTCCGGCTGTGAAGTCACTGAACAGAACGTCGCTGAT 1800 GGAGAAAGGGCTCCCGCAGAAGGAACGGCCTGTACCGTGCGCTCCGGCACAATCGCGTCT >>>>>>>>>>>>> 1860 CTTGTGTCTCACTCACGGAAAGAAACAACCTGAAGGCCATCCCGTCGGTCTGCACGTAAC >>>>>>> *************************************************** 1920 CGTGAAGACGTGTGGCCGCGTCCCACCTGCGGCTGGGTACCCTGCACCCGGCACTGTAGG ************************************************************ 1980 AGTCACGTGCAGCCTTTCTCAGGGGACTGTCATTGAAAAGGAAACGTTTGATGTCTGTGT ************************************************************ 2040 CAGCTGTCTTTGTAGTTAGGAAATAGATCCAATAAAGCCGTATTTTTTTGCTGGacaggc ************************************************************ 2100 gtagtctgcgagtggttcatgatacgcgtggaagatgccgctttgttctcagagtgtgtt ************************************************************ 2160 ttcagtggcgtgtacttggatcgtctgtgaaatgaacctcgtgttgggaaggctgtgtag ************************************************************ 2220 acgcggccattcgccgttggaagggcatcttgccagtagagctgttccctttcttctatg ************************************************* 2280 tttaggtaaaaacctgccgtagaaatttgcgagacgccggatagttcccaggccctgtaa <<<<<<<<<<<<<<<<<<<<< 2340 ctgaagcagctcagaaatgttcatccgggcgaggtggagaaggaactcctgctag KEYS (in order of precedence): XXXXXX excluded region ****** target >>>>>> left primer <<<<<< right primer ADDITIONAL OLIGOS start len tm gc% any 3' rep seq 1 LEFT PRIMER 1847 20 59.90 50.00 6.00 2.00 11.00 CACAATCGCGTCTCTTGTGT RIGHT PRIMER 2340 21 59.36 52.38 7.00 2.00 12.00 gttacagggcctgggaactat PRODUCT SIZE: 494, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 0.00 2 LEFT PRIMER 1847 21 61.85 52.38 6.00 1.00 12.00 CACAATCGCGTCTCTTGTGTC RIGHT PRIMER 2339 21 60.33 52.38 7.00 1.00 12.00 ttacagggcctgggaactatc PRODUCT SIZE: 493, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 0.00 3 LEFT PRIMER 1847 20 59.90 50.00 6.00 2.00 11.00 CACAATCGCGTCTCTTGTGT RIGHT PRIMER 2317 20 59.85 50.00 6.00 2.00 12.00 ggcgtctcgcaaatttctac PRODUCT SIZE: 471, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 2.00 4 LEFT PRIMER 1848 20 58.88 50.00 4.00 1.00 12.00 ACAATCGCGTCTCTTGTGTC RIGHT PRIMER 2339 21 60.33 52.38 7.00 1.00 12.00 ttacagggcctgggaactatc PRODUCT SIZE: 492, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 0.00 Statistics con too in in no tm tm high high high high sid many tar excl bad GC too too any 3' lib poly end ered Ns get reg GC% clamp low high compl compl sim X stab ok Left 3206 0 0 1573 516 0 0 0 2 522 49 0 65 479 Right 570 0 0 0 86 0 0 0 4 171 19 0 31 259 Pair Stats: considered 355, unacceptable product size 346, tm diff too large 1, ok 8 primer3 release 1.0